Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions

Microbiome-based classification models for fresh produce safety and quality evaluation

Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food.

IMPORTANCE

Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.

Sprouts as probiotic carriers: A new trend to improve consumer nutrition

Over the past few decades, efforts to eradicate hunger in the world have led to the generation of sustainable development goals to reduce poverty and inequality. It is estimated that the current coronavirus pandemic could add between 83 and 132 million to the total number of undernourished people in the world by 2021. Food insecurity is a contributing factor to the increase in malnutrition, overweight and obesity due to the quality of diets to which people have access. It is therefore necessary to develop functional foods that meet the needs of the population, such as the incorporation of sprouts in their formulation to enhance nutritional quality. Germination of grains and seeds can be used as a low-cost bioprocessing technique that provides higher nutritional value and better bioavailability of nutrients. Consequently, the manuscript describes relevant information about the germination process in different seeds, the changes caused in their nutritional value and the use of techniques within the imbibition phase to modify the metabolic profiles within the sprouts such as inoculation with lactic acid bacteria and yeasts, to generate a functional symbiotic food.

Immune-Boosting Potentiating Properties of Brassica nigra Hydroalcoholic Extract in Cyclophosphamide-Induced Immunosuppression in Rats

The antioxidative and immune-boosting properties of the hydroalcoholic extract of Brassica nigra sprouts in cyclophosphamide-induced immunosuppression in rats were investigated in this study. B. nigra sprouts were prepared in the lab to monitor the bio-changes in bioactive compounds during the sprouting period up to 7 days at 17 ± 1 °C and 90% relative humidity. The total phenolic content (TPC), antioxidant activity (AOA), total flavonoids (TFs), total flavonols (TFLs), and total carotenoids (TCs) were evaluated. Consequently, the identification and quantification of phenolic acids, their derivatives, and flavonoids were carried out using HPLC. Subsequently, the selected BN sprout (6-day-old sprout) was biologically examined, and oxidative stress biomarkers, hematological parameters, immunoglobulins (Igs), and pro-inflammatory and anti-inflammatory cytokines were investigated. An increase in TPC, AOA, TFs, TFLs, and TCs was observed by increasing the sprouting time. The HPLC analysis indicated that the B. nigra seeds contained 10 phenolic acids and 4 flavonoids, predominantly syringic acid and quercetin, respectively. After 3 days, the number of phenolic acids increased to 16, predominantly syringic acid, and the number of flavonoids increased to 7, predominantly quercetin. On the 6th day, 13 phenolic acids were estimated, with the highest being benzoic acid, and 6 flavonoids were estimated, with the highest being quercetin. The greatest rise in phenols was seen on the sixth day of sprouting. These included caffeic acid, chlorogenic acid, cinnamic acid, ferulic acid, coumaric acid, benzoic acid, and rosmarinic acid. Flavonoids such as kaempferol and myricetin increased. The sprouts on day 6 were recorded as having the highest bioactive compounds and AOA content. The selected B. nigra sprouts were examined for antioxidative and immunomodulatory properties in a rat model. Dosing 250 and 500 mg kg-1, the rats exhibited significant improvements in terms of antioxidative stress and the number of white blood cells (WBCs), lymphocytes, and neutrophils in the blood, indicating stimulation of the immune response in a dose-dependent manner. In addition, the production of immune proteins, such as IgG, IgM, and IgA, was enhanced in the blood. Moreover, the 500 mg kg-1 concentration of BN extract stimulated cytokine production in a stronger manner than the 250 mg kg-1 concentration, indicating that the extract significantly increased immune activity. In conclusion, the results indicate that mustard seed extracts have immunosuppressive properties against cyclophosphamide-induced immunosuppression in rats.

Analysis of Dynamics and Diversity of Microbial Community during Production of Germinated Brown Rice

Sprouts may be contaminated with different pathogenic and spoilage microorganisms, which lead far too easily to foodborne outbreaks. The elucidations of microbial profiles in germinated brown rice (BR) are important, but the changes in the microbial composition during germination are unknown. This study aimed to investigate the microbiota composition and to monitor the dominant microbial dynamics in BR during germination using both culture-independent and -dependent methods. BR samples (HLJ2 and HN) were collected from each stage of the germination processing. The populations of microbes (total viable counts, yeast/mold counts, Bacillus cereus, and Enterobacteriaceae) of two BR cultivars increased markedly with the prolongation of the germination time. High-throughput sequencing (HTS) showed that the germination process significantly influenced the microbial composition and reduced the microbial diversity. Similar microbial communities were observed between the HLJ2 and the HN samples, but with different microbial richness. The bacterial and fungal alpha diversity achieved the maximum for ungerminated samples and declined significantly after soaking and germination. During germination, Pantoea, Bacillus, and Cronobacter were the dominant bacterial genera, but Aspergillus, Rhizopus, and Coniothyrium dominated for the fungi in the BR samples. The predominance of harmful and spoilage microorganisms in BR during germination is mainly from contaminated seeds, which highlights the potential risk of foodborne illness from sprouted BR products. The results provide new insight into the microbiome dynamics of BR and may help to establish effective decontamination measures against pathogenic microorganisms during sprout production.

Comprehensive transcriptomic and metabolomic profiling reveals the differences between alfalfa sprouts germinated with or without light exposure

Alfalfa sprouts are among the most nutritionally rich foods, and light exposure is a critical factor in determining their biomass and quality. However, detailed metabolic and molecular differences between yellow and green alfalfa sprouts remain unclear. In this study, comprehensive metabolomic and transcriptomic analyses were integrated to evaluate the nutrient composition of alfalfa sprouts during germination with or without light exposure. Differentially expressed genes and differentially accumulated metabolites in green and yellow alfalfa sprouts were significantly enriched in secondary metabolic pathways, such as the isoflavonoid biosynthesis pathway. Green alfalfa sprouts contained a wide variety of lipids, flavonoids, phenolic acids, and terpenoids, among which the top three upregulated were calycosin, methyl gallate, and epicatechin 3-gallate, whereas yellow alfalfa sprouts contained relatively more isoquercitrin. These results provide new insights into the nutritional value and composition of alfalfa sprouts under different germination regimes.

Microbial Community, Fermentation Quality, and in vitro Degradability of Ensiling Caragana With Lactic Acid Bacteria and Rice Bran

This study aimed to assess the effects of microbial inoculants and growth stage on fermentation quality, microbial community, and in vitro degradability of Caragana silage from different varieties. Caragana intermedia (CI) and Caragana korshinskii (CK) harvested at the budding (BU) and blooming (BL) stages were used as raw materials to prepare silage, respectively. The silages at each growth stage were treated for ensiling alone (control), with 5% rice bran (RB), a combination of RB with commercial Lactobacillus plantarum (RB + LP), and a combination of RB with a selected strain Lactobacillus plantarum L694 (RB + L694). The results showed that the crude protein (CP) content of CI was higher than that of CK, and delay in harvest resulted in greater CP content in Caragana at BL stage. After 60 days of fermentation, the concentrations of lactic acid (LA) in the RB + L694 treatments were higher than those in control treatments (p < 0.05), while the pH, concentrations of NH3-N, neutral detergent fiber with the addition of α-amylase (aNDF) were lower than those in control treatments (p < 0.05). RB + L694 treatments could decrease acid detergent fiber (ADF) content except in CIBL. In CK silages, adding RB + L694 could reduce bacterial diversity and richness (p < 0.05). Compared with the control, RB + L694 treatment contained higher Lactobacillus and Enterobacter (p < 0.05). In vitro NDF and DM degradability (IVNDFD and IVDMD) was mostly affected by growth period, and additive RB + l694 treatment had higher IVDMD and lower IVNDFD than other treatments (p < 0.05). Consequently, the varieties, growth stages, and additives could influence the fermentation process, while the blooming stage should be selected in both Caragana. Furthermore, the results showed that RB and L. plantarum could exert a positive effect on fermentation quality of Caragana silage by shifting bacterial community composition, and RB + L694 treatments outperformed other additives.

The Microbial Quality of Commercial Chopped Romaine Lettuce Before and After the “Use By” Date

In the United States, due to the limited information about the microbial quality and safety of fresh produce after the labeled open dates, unnecessary discarding of fresh produce in good conditions and food loss have been caused. The aim of this study was to address this knowledge gap and evaluate the microbial quality of commercial chopped Romaine lettuce (RL) on the “Use By” dates (UBD) and 5 days after the “Use By” dates (UBD5). The microbial quality was evaluated using culture-dependent and culture-independent methods. Three brands of RL samples, from early and late harvest seasons, were purchased from local grocery stores and stored at 4°C until 5 days after their UBD. On the UBD and UBD5, bagged lettuce was opened, homogenized, diluted, and plated onto plate count agar and anaerobic agar to obtain total aerobic plate counts (APC) and total anaerobic plate counts (AnPC). For the culture-independent method, DNA was extracted from each sample homogenate and used for 16S rRNA gene sequencing. The culture-dependent results showed that there was no significant change in APC or AnPC between UBD and UBD5 samples. The APC and AnPC ranged from 5.71 ± 0.74 to 7.89 ± 0.10 Log CFU/g and 1.75 ± 0.08 to 7.32 ± 0.61 Log CFU/g, respectively. No significant difference in alpha diversity, based on observed features and Shannon index values, was detected between UBD and UBD5 samples using 16S rRNA sequencing. Similarly, no difference was observed in beta diversity based on the Jaccard distance matrixes and the weighted Unifrac distance matrixes. Taxonomic analysis revealed 128 genera in all RL samples. The top five genera were Pseudomonas (with relative abundance ranging from 16.47 to 92.72%), Serratia (0–52.35%), Weissella (0–42.42%), Pantoea (0.17–21.33%), and Lactococcus (0–24.30%). The differential abundance analysis based on the ANCOM test showed that no bacteria were detected to have significantly differential abundance in RL between UBD and UBD5. In summary, both the culture-dependent and culture-independent results showed that there was no significant difference in the microbial quality of RL before and shortly after the UBD.

Use of Phage Cocktail for Improving the Overall Microbiological Quality of Sprouts—Two Methods of Application

Background: the aim of this study was to improve the overall microbiological quality of five different sprouts (alfalfa, kale, lentil, sunflower, radish) using newly isolated bacteriophages. Method: in this study we had isolated from sewage 18 bacteriophages targeting bacteria dominant in sprouts. Five selected bacteriophage strains were photographed using a transmission electron microscope (TEM), and we analyzed the rate of attachment, resistance to chloroform, the burst size, and the latency period. Two methods of application of the phage cocktail were investigated: spraying, and an absorption pad. Results: the spraying method was significantly more efficient, and the maximum reduction effect after 48 h of incubation was 1.5 log CFU/g. Using pads soaked with phage lysate reduced the total number of bacteria to only about 0.27–0.79 log CFU/g. Conclusion: the reduction of bacteria levels in sprouts depended on the method of phage application. The blind strategy for searching phage targeting bacteria dominant in sprouts can be useful and economically beneficial as a starting point for further investigation in phage cocktail application for improving the overall microbiological quality of food. The main result of our research is to improve the overall quality of kale and radish sprouts by spraying them with a phage cocktail.

Plant sprout foods: Biological activities, health benefits, and bioavailability

Plant sprout foods exhibit a lot of biological activities including anti-inflammatory, antioxidative, anticancer, antidiabetes, anti-infection, and antiviral activities. Up to the present moment, plant sprout foods have received much attention due to their abundance, good bioavailability, and health benefits for human. This review highlights the biological activities of different plant sprout foods (viz., broccoli sprout, buckwheat sprout, wheat sprout, mung bean sprout, soybean sprout, and adkuzi bean sprout) using in vitro model, animal model, and human model. Furthermore, the bioavailability of plant sprout foods is also discussed. PRACTICAL APPLICATIONS: A review of the literature was conducted to biological activities of plant sprout foods, in addition to a summary of health benefits and bioavailability of sprout foods. Several biological activities of plant sprout foods with in vitro and in vivo evidence are currently unexplored in clinical trials, because the effects of sprout foods on human tissues and cells measured by tube test do not recapitulate the actual in vivo effects. Moreover, the safety of chemoprevention strategies using sprout foods that to protect against environmental exposures and other oxidative stress-related pathologies is important. Further research is warranted to evaluate bioavailability of individual forms.

Antilisterial Activity of Bacteriocins Produced by Lactic Bacteria Isolated from Dairy Products

Sixty-nine Lactic Acid Bacteria (LAB) and bifidobacteria were isolated and identified from Italian dairy products (raw milk, cream, butter, soft cheese and yoghurt) to find new antimicrobial compounds to use as food bio-preservatives. All the isolates were preliminarily screened by the deferred antagonism method for bacteriocin production. Afterwards, to evaluate the release of bacteriocin in liquid medium, the Cell-Free Supernatant Fluid (CFSF) of the best producers was tested by agar well diffusion assay. The study allowed the selection of three bacteriocin producing strains (Enterococcus faecium E23, Bifidobacterium thermophilum B23 and Lactobacillus bulgaricus L21), endowed with the strongest and broadest inhibitory capability against the pathogen Listeria monocytogenes. The molecular characteristics and the chemical–physical properties of both producers and the respective bacteriocins were studied and compared. The results showed that E. faecium E23 was the best producer strain and its class IIa bacteriocins, called enterocin E23, exhibited a good spectrum of activity towards L. monocytogenes. Enterocin E23 was stable over a wide range of pH and at low temperatures for at least four months and, for this reason, it can be employed in refrigerated foods for the control of L. monocytogenes, the major concern in dairy products.

Enantiomeric effect of paclobutrazol on the microorganism composition during wine fermentation

Pesticide residues in food can bring potential risks to human health and has been widely concerned in recent years. In the current study, the influence of paclobutrazol, which resided in raw material (grape) on wine fermentation process, were investigated. The degradation kinetic results indicated that the enantiomers of paclobutrazol not be degraded during 30 days of fermentation process. In order to achieve the fermented microorganism information of diversity, community composition, and function, the analysis of 16S rRNA and ITS sequencing were performed. Results demonstrated that the dominant microorganisms multiplied and the microbial diversity in the samples decreased as the fermentation process progresses. Furthermore, the paclobutrazol stimulated the growth of Pichia, which was observed during wine fermentation and which may have an underlying impact on the quality of the wine. The above results inferred that paclobutrazol residue could disturb the microbial community stability during wine fermentation, and the stable existence of paclobutrazol will cause potential risks to food safety and human health. In this work, we have successfully devised a method to investigate the influences of pesticide residues in raw materials during food processing and conclusions from this study could provide basis for dietary risk assessment.